[MINC-users] How to register T1 onto T2/PD?

[D. Louis Collins]

Ed,

mritoself uses mutual information as an objective function to  
establish the mapping between the two scans to be registered.  This  
works well when you have a decent estimate of the initial  
transformation to ensure that you are in the local minima of the  
objective function.  mritoself will fail in the way you describe if  
the initial estimate (either given by the use, or estimated by the  
procedure) is not good.

If your datasets were acquired during the same session, and the  
subject did not move much during the session, then try
	mritoself -close T1.mnc T2.mnc T1_to_T2.xfm

If the datasets were acquired during different sessions, then the two  
datasets will be reasonably far from one another.  if so, try
	 mritoself -far T1.mnc T2.mnc T1_to_T2.xfm	

If neither of these work, then you'll have to estimate the initial  
transformation by hand. do the following
	register T2.mnc T1.mnc
	identify homologous tag points in each data set
	save the transformation as initial_t1-to-t2.xfm

then
	mritotal -transform initial_t1-to-t2.xfm T1.mnc T2.mnc T1_to_T2.xfm

hope this helps.

-Louis

On Oct 17, 2008, at 8:25 AM, Ed Gronenschild wrote:

> Hi,
>
> I need to register a coronal T1 stack onto an axial T2 stack
> of the same subject. Details of the stacks are:
> T1:
> 176 slices of 384 * 384 pixels, pixel size = 0.67 mm * 0.67 mm,
> slice thickness = 1.34 mm.
>
> T2:
> 50 slices of 256 * 256 pixels, pixel size = 1.0 mm * 1.0 mm,
> slice thickness = 2.00 mm
>
> The T2 slices are positioned such that they cover only the brain
> tissue (in the Z direction), whereas the T1 slices cover a much
> larger area, fully including the head and part of the neck.
>
> I tried the following two commands:
>
> mritoself T1.mnc T2.mnc T1_to_T2.xfm
> mincresample -transformation T1_to_T2.xfm -like T2.mnc \
> 	T1.mnc T1_to_T2.mnc
>
> That produced a stack that is incorrect in that it is shifted
> along the Z-axis.
>
> The same is true if I use a PD stack with the same size and
> orientation as T2.
>
> It looks as if the problem is mainly caused by the difference
> in extent of both stacks (mainly in the Z-direction).
> Is there another command to register a T1 onto a T2 or PD?
>
> Ed
>
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